Deus Ex games, Prey, Chronicles of Riddick, Singularity, Timeshift, ...I enjoyed all of them ;)
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Planetside 2 is sweet.
Republic Commando is an awesome star wars squad shooters.
FTL, I believe mentioned below, is a really awesome starship command roguelike, really fun.
Gratuitous Space Battles is kinda cool, a space RTS where you design ships and formations but don't control the battle. Dead Space is sci-fi horror. SPAZ is a pretty cool indie spaceship game.
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Aliens versus Predator from 2010 was actually quite enjoyable :)
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Ok then some less popular games:
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Beneath a Steel Sky
Gemini Rue
The Longest Journey
Resonance
Space Quest
Waking Mars
Xenosaga
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Not yet mentioned:
Sins of A Solar Empire
Supreme Commander
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Chrome + Chrome Spec Force
Deus Ex series
Serious Sam series
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Oh boy, here have some suggestions:
E.Y.E. Divine Cybermancy - Do you know what's happening in this game? No. But that's okay, cause you'll like it anyway.
FTL - BUY THIS NOW, RIGHT NOW (while its on sale, and get it from the developers as it gives you a drm-free copy for you humble library and a steam key)
Waking Mars - A great game.
Primordia - Scifi point and click adventure. I hear good things.
S.P.A.Z. - Fun, although gets to be a bit of a slog halfway through. On sale right now though for the Linux sale.
Miner Wars 2081 - Descent 2012.
Retrovirus - Descent 2013.
Beyond Good & Evil - An older action/adventure game, very good.
System Shock 2 - Now on gog!
Gimbal - A great top-down space shooter on greenlight
Fallout: New Vegas - Maybe not the kind of sci-fi you're looking for, and definitely mainstream, but if you haven't played this you should rectify that...
Natural Selection 2 - Alien v. Human multiplayer game.
Command & Conquer 3 - Mainstay of RTS.
Endless Space - Space 4X Strategy.
Sins of a Solar Empire - More Space Strategy!
AI War: Fleet Command - EVEN MORE SPACE STRATEGY.
Also, these aren't out yet but you might be interested in them:
Planetary Annihilation - A Kickstarted RTS game that will involve mutliple planets and galaxies as the battlefields. From the makers of Total Annhiliation.
Starbound - From one of the makers of Terraria, a similar pixely game, but in space and with a ton of content and procedurally generated planets.
Star Command - A Star Trek-like isometric build and fight spaceships game.
Routine - FPS-stlye moonbase horror. Greenlit, should be out soon.
Kinetic Void - Also greenlit but awaiting release, this is a 3D space fighter/simulator with a focus on complete spaceship customization.
Hope you find something :)
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I'd say Omikron and Anachronox. Especially Anachronox. If you're into point and click though, go for Gemini Rue, or if you're a hardcore fan of the genre try and hunt down The Ward (won't be easy...) or download 6 Days a Skeptic (hope that's the right title), or pick up The Dig on Steam (bit of a pixel hunt there though).
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Could You recommend some good sci-fi games (not a big fan of flight sims and MMO/F2P)? Played most of mainstream games (Mass Effect, XCOM, Syndicate, Crysis, Bulletstorm, W40k games etc.), so I'm looking for less popular titles.
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